A multi-omics study of bacterial growth arrest in a synthetic biology application

Scaling up the functioning of synthetic circuits from microplates to bioreactors is far from trivial to achieve. We here test the scalability performance of a previously developed growth switch for increasing product yields in bacteria, based on external control of RNA polymerase expression. We show that, in liter-scale bioreactors operating in fed-batch mode, growth-arrested Escherichia coli cells are able to convert glucose to glycerol at an increased yield. A multi-omics quantification of the physiology of the cells shows that apart from acetate production, few metabolic side-effects occur, while a number of specific responses to growth slow-down and growth arrest are launched on the transcriptional level. These responses include the downregulation of genes involved in growth-associated processes, such as amino acid and nucleotide metabolism and translation, and the upregulation of a heat response. Interestingly, these transcriptional responses are buffered on the proteomic level, probably due to the strong decrease of the total mRNA concentration after the diminution of transcriptional activity and the absence of growth dilution of proteins. This transforms the growth-arrested cells into “bags of proteins“ with a functioning metabolism. More generally, the analysis shows that physiological characterization of bacterial cells hosting a synthetic circuit may reveal complex patterns of adaptation on different time-scales, dynamically interacting with the bioreactor environment. mRNA profiles of E. coli wild-type and growth-arrested cells carrying a plasmid for glycerol production (W-gly vs R-gly)